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大麻状罗布麻的全基因组分析和 SSR 标记开发
作者:
作者单位:

1宁夏大学西北土地退化与生态恢复国家重点实验室培育基地，银川 750021;2宁夏大学西北退化生态系统恢复与重建教育部重点实验室，银川 750021

基金项目:

国家重点研发计划资助(2017YFC0504406)


Whole Genome Sequencing and Development of SSR Markers in Apocynum cannabinum
Author:
  • SONG Li-xiao 1,2

    SONG Li-xiao

    1 Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan 750021; 2 Key Laboratory for Recovery and Restoration of Degraded Ecosystem in North-western China of Ministry of Education, Ningxia University, Yinchuan 750021
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  • LI Guo-qi 1,2

    LI Guo-qi

    1 Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan 750021; 2 Key Laboratory for Recovery and Restoration of Degraded Ecosystem in North-western China of Ministry of Education, Ningxia University, Yinchuan 750021
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  • JIN Chang-qing 1,2

    JIN Chang-qing

    1 Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan 750021; 2 Key Laboratory for Recovery and Restoration of Degraded Ecosystem in North-western China of Ministry of Education, Ningxia University, Yinchuan 750021
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  • GONG Shi-pei 1,2

    GONG Shi-pei

    1 Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan 750021; 2 Key Laboratory for Recovery and Restoration of Degraded Ecosystem in North-western China of Ministry of Education, Ningxia University, Yinchuan 750021
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Affiliation:

1 Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan 750021;2 Key Laboratory for Recovery and Restoration of Degraded Ecosystem in North-western China of Ministry of Education, Ningxia University, Yinchuan 750021

Fund Project:

National Key R&D Program of China (2017YFC0504406)

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    摘要:

    大麻状罗布麻是重要的经济和生态作物，但是其基因组缺乏和分子标记少限制遗传研究工作的开展。本研究利用Illumina测序平台对大麻状罗布麻的基因组大小进行测定，通过生物信息学方法对其基因组杂合度和重复序列等基本信息进行预估，并做了基因组的初步组装，在此基础上并对其基因组序列进行了SSR查找。研究结果表明，总测序量为31.94 Gb，测序质量正常(Q20≥90%，Q30≥85%)，与NCBI核苷酸数据库(NT)比对显示样本不存在外源污染；K-mer分析(K=17)结果显示，大麻状罗布麻基因组大小为239.02 Mbp，杂合率为0.56%，重复序列占全基因组比例为36.72%，初步预估大麻状罗布麻基因组为复杂基因组；采用K-mer=41进行基因组初步组装，共获得273,336条contigs，N50为3,838 bp，总长为222,723,253 bp，进一步将contigs进行连接、延长，组装得到224,587条scaffolds，N50为6,421 bp，总长为226,378,236 bp；此外，对基因组数据进行SSR分子遗传标记分析，共鉴定出117,511个SSR，不同类型核苷酸重复差异较大，单核苷酸重复最多，六核苷酸重复最少。该研究为后续全基因组de novo测序及组装策略提供依据。

    Abstract:

    Apocynum cannabinum is an important economic and ecological crop. Genetic studies on this crop remains largely behind due to the un-availability of genome reference and limited amount of molecular markers. In this study, we performed a whole genome sequencing of?A. cannabinum?by sequencing technology (Illumina), and analyzed the ratios of heterogeneity and repetitive elements, followed by exploration of SSR markers. A total of 31.94 Gb high-quality sequences (Q20 ≥ 90% and Q30 ≥ 85%) have been generated. By searches with NCBI nucleotide database (NT), no exogenous contamination in the sample was detected. De novo assembly and K-mer analysis revealed a genome size of 239.02 Mbp, with 0.56% heterozygosity and 36.72% of repetitive sequences. 273,336 contigs with a N50 of 3,838 bp in length have been detected, and the total length was 222,723,253 bp. 224,587 scaffolds were further assembled, with a N50 of 6,421 bp in length, and the total length was 226,378,236 bp. By predicting for the simple sequence repeats (SSR), 117,511 have been detected potentially for exploring SSR markers. Of all SSR categories, the mononucleotide and hexanucleotide repeat units formed the largest and the least categories, respectively. Thus, this work generated a sequence dataset that might be useful source for future?de novo assembling of?A. cannabinum genome.

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宋立肖,李国旗,靳长青,等.大麻状罗布麻的全基因组分析和 SSR 标记开发[J].植物遗传资源学报,2019,20(5):1309-1316.

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  • 收稿日期:2018-12-18
  • 最后修改日期:2019-01-07
  • 录用日期:2019-01-18
  • 在线发布日期: 2019-09-17
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